BACKGROUND: Roux-en-Y gastric bypass (RYGB) for clinically severe obesity (CSO) results in a 'paradoxical' response of the measured resting energy expenditure (MREE) in which the MREE remains within the predicted range based upon the Harris-Benedict (HB) equation, despite a significant decrease in caloric intake to 500-1000 kcal/day. The mechanism for this response is unknown. A study was undertaken to determine whether the changes in MREE after RYGB are related to limb-length of the gastric bypass. METHODS: A prospective clinical trial of varying limb-lengths based on body mass index (BMI) in patients having RYGB for CSO. The records of patients who underwent RYGB for CSO and had MREE measured at baseline, 6 months and 12 months postoperation were reviewed. MREE was performed using a Med Graphics CCM system after an overnight fast or at least 4 hours after a light meal, and a 30 minute rest in a supine position in a neutral environment, on the same day of the week between the hours of 10 a.m. and 4 p.m. Patients were selected for RYGB in accordance with NIH recommendations. RYGB was performed in a standardized fashion with the Roux limb-length varied as follows: (A) BMI < or = 51 kg/m2 - 75 cm limb (n = 20); (B) BMI < or = 51 kg/m2 - 150 cm limb (n = 16); (C) BMI > or = 51 kg/m2 - 150 cm limb (n = 18); or (D) BMI > or = 51 kg/m2 - 250 cm limb (n = 6). RESULTS: Data from 60 patients (nine male, 51 female; mean age 39 years; mean baseline BMI 51.5 +/- 10 kg/m2; mean baseline weight 145 +/- 32 kg) were analyzed. There were no significant differences in MREE or percentage HB-predicted energy expenditure between the groups. CONCLUSIONS: These data suggest that the observed changes in MREE following RYGB for CSO are not related to the limb-length of the bypass.